Palettes

Palettes

Below is a collection of palettes for use in the app or in reports.

# Initilize libraries
library(ggplot2)
# Utility function to display palette
library(scales)

#Palettes
library(RColorBrewer)
library(viridisLite)
library(ggsci)
library(Polychrome)

Categorical Palettes

Palletes from ggsci package

The ggsci package contains several categorical palettes inspired by scientific journals and science fiction. The palettes usually contain 7-10 colors, and they can be extended with colorRampPalette().

# AAAS colors: only 10 present
show_col(pal_aaas("default")(10))

# Extend to 20 colors
show_col(
  colorRampPalette(
    # Original 10 colors (pal_aaas("default") returns a function, to which
    # n is passed)
    pal_aaas("default")(10)
    )(20)
  )

# This is a deterministic approach (same results are returned each time the function is ran)

# Nature Publishing Group Palette: Original 10 colors
show_col(pal_npg("nrc")(10))

# Extend Nature Publishing Group Palette
show_col(
  colorRampPalette(
    # Original 10 colors 
    pal_npg("nrc")(10)
    # Call '20' from function produced to get 20 colors
    )(20)
  )

# NJEM Pallete
# Original Colors
original <- pal_nejm()(8)
show_col(original)

# Extended Colors
show_col(colorRampPalette(original)(20))

# Lancet Pallete
# Original Colors
original <- pal_lancet()(9)
show_col(original)

# Extended Colors
show_col(colorRampPalette(original)(20))

# JAMA palette
# Original Colors
original <- pal_jama()(7)
show_col(original)

# Extended Colors
show_col(colorRampPalette(original)(20))

# Journal of Clinical Oncology Pallette
# Original Colors
original <- pal_jco()(10)
show_col(original)

# Extended Colors
show_col(colorRampPalette(original)(20))

# UCSC Genome Browser Palette
# Original palette has 26 colors; does not need extending
show_col(pal_ucscgb()(26))

# D3.js Palette
# D3 is a JavaScript library for interactive data 
# visualization (https://d3js.org/)
# Original Colors
original <- pal_d3("category10")(10)
show_col(original)

# Extended Colors
show_col(colorRampPalette(original)(20))

# Three 20 color palettes exist for D3
show_col(pal_d3("category20")(20))

show_col(pal_d3("category20b")(20))

show_col(pal_d3("category20c")(20))

# LocusZoom plaette
# Original Colors
original <- pal_locuszoom()(7)
show_col(original)

# Extended Colors
show_col(colorRampPalette(original)(20))

# Integrated Genomics Viewer Palette
# Original palette has 51 colors
# Variable name is used in title output by swatch() 
`IGV Palette` <- pal_igv()(51)
swatch(`IGV Palette`)

# 20-color subset
original <- pal_igv()(20)
show_col(original)

# University of Chicago Palette
# Three palettes provided in pal_uchicago
for (pal_opt in c("default", "light", "dark")){
  # Original Colors
  original <- pal_uchicago(pal_opt)(9)
  show_col(original)

  # Extended Colors
  show_col(colorRampPalette(original)(20))
}

# Star Trek Palette
# Original Colors
original <- pal_startrek()(7)
show_col(original)

# Extended Colors
show_col(colorRampPalette(original)(20))

# Rick and Morty Palette
# Original Colors
original <- pal_rickandmorty("schwifty")(12)
show_col(original)

# Extended Colors
show_col(colorRampPalette(original)(20))

# University of Colorado Palette
# A palette created in-house using the official colors of CU
# (https://www.colorado.edu/brand/how-use/color)
colors <- c("#CFB87C", "#000000", "#565A5C", "#A2A4A3")
# Original colors
show_col(colors)

# Extended colors
show_col(colorRampPalette(colors)(20))

# This makes a nice continuous palette

# Additional colors in CU Palette
cu_extended <-
  colors <- c(
    # First four: official CU Colors
    "#CFB87C", 
    "#000000", 
    "#565A5C", 
    "#A2A4A3",
    # Color of walls on most campus buildings 
    "#AD7B64",
    # Color of many roofs on campus
    "#9A4A3A",
    # Color of pine trees in Flatirons
    "#3A553A",
    # Color of the sky on a sunny day
    "#529FDF"
    )

show_col(cu_extended)

# Extend to 20 colors
show_col(colorRampPalette(cu_extended)(20))